When clearing an invoice with a receipt, it doesn’t seem to clear the payment properly. Going to the Receipts and Payments screen, the payment still shows as overdue. If I then close Manager and go back in, sometimes the payment shows as cleared properly. I am fairly new to this so maybe something I am doing wrong so any pointers would be useful. Sating that, why would it sometimes show correctly and other times as overdue on the same payment?
You need to post screen images of what you are doing. It sounds like you are not entering the payments in the right manner.
Are you saying that the status goes back and forth on the same invoice? Or that sometimes things are applied correctly and sometimes not?
The status changes in the payments and receipts screen on the same invoice. As stated, sometimes it shows as overdue and on others applied ok. It seems that it changes when restarting Manager. It doesn’t do it during a session of use
This sounds like you might be entering transactions in two different copies of your business data file, so that a receipt entered in one copy does not appear in another. This can happen, for example, if you open a data file directly in a remote location (like Dropbox) versus opening from the Businesses page. It can also happen if you open a backup file and make entries there. Manager does not synchronize content between multiple versions of a business data file.
Can you describe your setup and work practices more fully? Have you modified the default location of the application data folder? Have you made backups and, if so, how have you used them?
Also, you did not specifically state whether this is happening with sales invoices or purchase invoices. You mentioned payments, which implies you are paying suppliers’ purchase invoices. But users often use that term when they mean receipts.
I will also point out that overdue status does not appear in the Receipts & Payments tab. Status appears in the Sales Invoices and Purchase Invoices tabs.
So precise descriptions of problems are necessary before anyone can help. Screen shots to illustrate the discrepancies you say you are experiencing would also help. Use them, for example, to illustrate changes on the Summary page when this problem occurs, compared to when it does not. And show the Edit screen of a transaction you believe is not correctly presented.
I do apologise for my lack of understanding of precise terminology but understand what you mean. I do back up the database to a dropbox file but have never reinstated it as yet so it is purely just a back up.
The overdue message does appear on the Sales Invoice page but on the Receipts and Payments screen, it shows as a payment received. Sorry, but I cant see how to include a screenshot on here
Use the upload arrow above the composing pane: 
Of course, capturing the screen shot depends on your operating system.
Thank you.
This is the process I follow
1 Create invoice
2 Email Invoice internally with Email tab
3 WHen Payment is received, open invoice and click on view for the invoice I have received payment for
4 Click Receipt button at the top
5 Change account to my bank account
6 Change the account box lower down to Sales (Default is accounts receivable)
7 Click create
If you look at the screen shots, the £99.50 shows as overdue even though the payments screen shows its paid.
I’m sure I’m doing something wronf but can’t see what
You have raised an invoice for the rent, presumably, of Room 5 in favour of a customer X
The accounting entries are
Debit Account receivables/customer X
Credit Sales or whatever account you entered on the invoice
You then receive the payment and the entries SHOULD BE
Debit Bank account
Credir Account Receivables/customer X
But you seem to change the account to Sales so now you have the Sales x 2 and the customer x still owes you the full amount
You should not change the default account from Account Receivables but just select the customer and invoice if you want to allocate the payment to a particular invoice
All is explained in the Guides
@joe91 has it right, @bartona. You have not recorded the receipt against the sales invoice. You have, instead, recorded it as thought you made a separate, non-credit sale. Just because the receipt has been lodged in your bank account does not mean it has been associated with the sale receipt (since you severed that link when you posted the receipt to Sales. The sales invoice already posted the amount to Sales. The receipt just clears the debt owed by the customer because of the sales invoice.
None of this would cause a sales invoice status to toggle between paid in full and overdue (or any other status), however. And that was the problem you originally reported.
Thank you both for your help here. As I say, this is all new to me and gradually getting my head around it all. My mistake. I thought you recorded it against the sale. Think I get it now.
Thank you both again